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Sample GSM874809 Query DataSets for GSM874809
Status Public on Dec 20, 2012
Title OV3337_CGH
Sample type genomic
 
Channel 1
Source name universal reference
Organism Homo sapiens
Characteristics reference: universal reference
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name OV3337
Organism Homo sapiens
Characteristics tissue: Primary tumor, Ovarian
age: 64 years
tumor histology: serous
grade of tumor: 2
event (alive=1, dead=2): 2
progression (no progression=1, progression=2): 2
overall survival (os, n=months): 143.26
progression-free survival (pfs, n=months): 38.82
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol Scanner Model: GenePix 4000A
Description Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/43884.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Feb 13, 2012
Last update date Dec 20, 2012
Contact name Aslaug Helland
E-mail(s) [email protected]
Phone +47-22934431
Organization name Institute for Cancer Research, Oslo University
Department Dept of Genetics
Street address Hospital Radiumhospitalet
City Oslo
ZIP/Postal code 0310
Country Norway
 
Platform ID GPL3528
Series (1)
GSE35783 CGH-arrays ovarian serous carcinomas.

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2
VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE
1 398 397 184 187 214 210 389 387 196 195 205 200 0 0 121 139 69 84 91 83 75 66 424 405 1.019 .981 .976 1.215 1.095 2.192 12 90 1.296 .76 50 1890 5540 39 44 38 43 0 396 187 210 .98 386 200 1.021 .974 -.029 -.038
2 442 557 182 191 260 366 471 529 198 203 289 338 0 0 116 148 105 55 83 100 66 100 626 627 .71 1.408 1.17 1.478 1.346 1.656 12 90 1.511 .79 50 2040 5540 39 44 53 58 0 556 191 365 1.406 528 337 .711 1.168 .491 .224
3 218 231 181 191 37 40 192 207 184 192 11 16 0 0 116 89 41 48 26 26 15 11 77 27 .925 1.081 1.455 1.069 1.189 3.951 52 290 .802 .57 80 2180 5560 40 48 66 74 -50 231 191 40 1.079 207 16 .926 1.452 .11 .538
4 242 252 179 184 63 68 216 228 182 187 37 44 0 0 96 97 40 48 48 48 38 30 131 81 .926 1.079 1.189 1.176 1.125 2.776 52 276 1.148 .51 80 2330 5560 40 48 81 89 -50 252 184 68 1.078 228 44 .928 1.187 .108 .248
5 598 698 187 187 411 511 587 725 188 189 400 538 0 0 225 220 36 46 96 100 90 100 922 938 .804 1.243 1.345 1.311 1.204 1.821 32 164 1.166 .88 60 2480 5560 41 47 97 103 0 697 187 510 1.241 724 537 .806 1.343 .312 .425
6 254 280 184 186 70 94 226 250 188 187 42 64 0 0 93 109 44 47 48 57 36 42 164 106 .745 1.343 1.524 1.043 1.132 3.42 52 279 1.345 .64 80 2620 5560 40 48 110 118 -50 280 186 94 1.341 250 64 .746 1.521 .423 .605
7 218 228 182 186 36 42 198 214 186 191 16 28 0 0 70 72 44 49 32 34 17 21 78 44 .857 1.167 1.75 1.349 1.336 4.253 52 289 1.09 .19 80 2770 5560 40 48 125 133 -50 228 186 42 1.165 214 28 .858 1.747 .22 .805
8 500 620 184 185 316 435 482 623 190 197 298 438 0 0 135 147 41 56 100 100 91 100 751 736 .726 1.377 1.47 1.472 1.271 2.033 12 98 1.278 .84 50 2910 5550 40 45 140 145 0 619 185 434 1.374 622 437 .728 1.468 .459 .553
9 993 747 188 189 805 558 1010 741 189 192 822 552 0 0 244 123 43 48 100 100 96 100 1363 1374 1.443 .693 .672 .738 .68 1.669 32 236 .635 .9 70 3060 5560 40 47 154 161 0 746 189 557 .692 740 551 1.445 .671 -.531 -.577
10 385 408 178 193 207 215 381 409 183 197 203 216 0 0 124 114 41 46 84 90 84 87 422 419 .963 1.039 1.064 1.013 .935 2.725 32 170 1.027 .74 60 3210 5560 41 47 170 176 0 407 193 215 1.037 408 216 .964 1.062 .053 .087
11 860 698 195 190 665 508 902 719 197 190 707 529 0 0 190 105 49 44 96 100 96 100 1173 1236 1.309 .764 .748 .825 .723 1.817 32 227 .672 .88 70 3350 5560 40 47 183 190 0 697 190 507 .763 718 528 1.311 .747 -.391 -.421
12 656 663 184 184 472 479 722 709 189 186 538 525 0 0 227 198 40 43 90 100 90 93 951 1063 .985 1.015 .976 1.069 .995 2.708 32 160 .954 .85 60 3500 5550 40 46 199 205 0 662 184 478 1.013 708 524 .987 .974 .019 -.037
13 660 641 190 187 470 454 683 638 200 216 493 451 0 0 120 203 67 92 100 100 100 91 924 944 1.035 .966 .915 .898 .987 1.651 12 80 1.091 .81 50 3640 5530 38 43 213 218 0 640 187 453 .964 637 450 1.037 .913 -.052 -.131
14 467 591 179 186 288 405 486 596 181 188 307 410 0 0 122 158 40 43 96 96 90 96 693 717 .711 1.406 1.336 1.347 1.433 1.987 32 160 1.459 .83 60 3790 5550 40 46 228 234 0 590 186 404 1.404 595 409 .712 1.333 .49 .415
15 837 947 186 190 651 757 894 1024 188 192 708 834 0 0 209 286 43 50 100 100 100 93 1408 1542 .86 1.163 1.178 1.094 1.128 1.852 32 160 1.211 .9 60 3940 5550 40 46 243 249 0 946 190 756 1.161 1022 833 .861 1.176 .215 .234
16 2662 2421 180 195 2482 2226 2918 2655 189 196 2738 2460 0 0 1056 641 63 49 100 100 96 100 4708 5198 1.115 .897 .898 1.112 .852 2.221 32 220 .831 .93 70 4080 5550 39 46 256 263 0 2417 195 2223 .895 2651 2456 1.117 .897 -.159 -.157
17 1095 1385 187 201 908 1184 1180 1384 243 256 993 1183 0 0 317 306 218 237 90 100 90 96 2092 2176 .767 1.304 1.191 1.512 1.234 2.322 32 209 1.229 .91 70 4230 5540 38 45 271 278 0 1383 201 1182 1.302 1382 1181 .768 1.19 .381 .25
18 200 202 184 199 16 3 192 191 197 210 8 -8 0 0 49 56 102 94 7 7 0 0 19 0 5.333 .188 null 1.404 1.652 2.956 52 291 3.562 .15 80 4370 5560 40 48 285 293 -50 202 199 3 .187 191 -8 5.341 null -2.417 null
19 2438 2804 193 209 2245 2595 2993 3188 197 215 2800 2979 0 0 1187 1154 48 52 96 96 93 96 4840 5779 .865 1.156 1.064 1.283 1.152 2.308 32 213 1.092 .93 70 4520 5560 40 47 300 307 0 2800 209 2591 1.154 3183 2974 .866 1.062 .207 .087
20 1314 982 195 198 1119 784 1343 968 197 202 1148 770 0 0 222 152 45 53 100 100 100 100 1903 1918 1.427 .701 .671 .703 .686 1.334 80 507 .67 .92 110 4680 5550 37 48 314 325 0 981 198 783 .7 967 769 1.429 .67 -.515 -.578

Total number of rows: 43104

Table truncated, full table size 9758 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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